9-61192723-C-T

Variant names:

• chr9-61192723-C-T
• rs1471439864
• NM_015667.2:c.637C>T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015667.2(SPATA31A7):​c.637C>T​(p.Pro213Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0032 (5 hom., cov: 6)
  • Exomes 𝑓: 0.0042 (510 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31A7 NM_015667.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.06

Genes affected

SPATA31A7 (HGNC:32007): (SPATA31 subfamily A member 7) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0032767057).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31A7	NM_015667.2	c.637C>T	p.Pro213Ser	missense_variant	Exon 4 of 4	ENST00000619167.2	NP_056482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31A7	ENST00000619167.2	c.637C>T	p.Pro213Ser	missense_variant	Exon 4 of 4	1	NM_015667.2	ENSP00000484807.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 124 AN: 38520 Hom.: 5 Cov.: 6 FAILED QC

Gnomad AFR AF: 0.000580

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00158

Gnomad ASJ AF: 0.000822

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.00302

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00200

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00416 AC: 3609 AN: 866964 Hom.: 510 Cov.: 12 AF XY: 0.00399 AC XY: 1750 AN XY: 439124

Gnomad4 AFR exome AF: 0.000710

Gnomad4 AMR exome AF: 0.00323

Gnomad4 ASJ exome AF: 0.000685

Gnomad4 EAS exome AF: 0.0942

Gnomad4 SAS exome AF: 0.00150

Gnomad4 FIN exome AF: 0.0000835

Gnomad4 NFE exome AF: 0.0000976

Gnomad4 OTH exome AF: 0.00620

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00321 AC: 124 AN: 38576 Hom.: 5 Cov.: 6 AF XY: 0.00322 AC XY: 57 AN XY: 17726

Gnomad4 AFR AF: 0.000577

Gnomad4 AMR AF: 0.00158

Gnomad4 ASJ AF: 0.000822

Gnomad4 EAS AF: 0.0972

Gnomad4 SAS AF: 0.00300

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00198

Alfa AF: 0.00118 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 01, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.637C>T (p.P213S) alteration is located in exon 4 (coding exon 4) of the SPATA31A7 gene. This alteration results from a C to T substitution at nucleotide position 637, causing the proline (P) at amino acid position 213 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.030
DANN	Benign	0.26
DEOGEN2	Benign	0.027	T
LIST_S2	Benign	0.49	T
MetaRNN	Benign	0.0033	T
Sift4G	Benign	0.54	T
Vest4		0.090
gMVP		0.10

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1471439864; hg19: chr9-43628050;